Here it is. However, contrary to my first understanding, the problems assert themselves not only during, but also before the system upgrade (installation of additional programs made impossible etc.).

ok, thanks for sharing.
In my answer, I mainly referred to offical repos, while you probably meant third-party repos. If a package is in the *official* Ubuntu repos, or in some widely adopted third-party ones such as Medibuntu, then this should be your first choice, no doubt on that. If instead you have to choose between some strange third-party PPA or compiling from source, then you are right that the choice is not that clear, and both may land you into some dependency hell.